Development of flexible and transparent detection platforms using surface-enhanced Raman spectroscopy has emerged as an intense research field due to the demand for in-situ, real-time analysis. Herein, we present the fabrication of soft and ultra-thin substrates composed of silver nanoparticles that are photoreduced on nanotips-equipped ferroelectric templates and then transferred to the poly(methyl methacrylate) film for ultrasensitive detection of antibiotics, nitrofurantoin and nifuroxazide. Compared with the conventional ferroelectric templates, the utilization of nanotips-equipped ferroelectric template boosts the effective mass transfer of dense silver nanoparticles to the polymeric film, which can effectively enhance the Raman performance through the electromagnetic mechanism. The produced substrate shows excellent performance for the detection of antibiotics, including ultra-low limit of detection in the order of 10−12 M, high enhancement factor about 1010, excellent sensitivity, superior reproducibility and uniformity. Besides, the quantitative multiplex detection of nitrofurantoin and nifuroxazide is demonstrated to discriminate the five-order concentration difference. The practicality of the developed substrate is proved by the detection of nitrofurantoin and nifuroxazide on fish surfaces by utilizing the fiber-coupled Raman probe with the limit of detection of 2.08 × 10−10 M and 1.25 × 10−9 M The proposed detection strategy can be applied to perform the in-situ, real-time analysis for the identification of antibiotics in environmental samples.